#Figures for Quaeck-Davies et al PeerJ submission
setwd("")

#Fig 1: eye lens allometry
F1data<- read.table("TL_LD.txt", header = TRUE, fill=TRUE)


par(mfrow=c(2,2))

plot(F1data$TL[F1data$Sp=="A.carbo"], F1data$LensD[F1data$Sp=="A.carbo"], pch=19, xlab="Total Length (mm)", ylab="Lens Diameter (mm)")
LmAC<-lm(F1data$LensD[F1data$Sp=="A.carbo"]~F1data$TL[F1data$Sp=="A.carbo"])
abline(LmAC, col="red", lty=2)

plot(F1data$TL[F1data$Sp=="C.rupestris"], F1data$LensD[F1data$Sp=="C.rupestris"], pch=19, xlab="Total Length (mm)", ylab="Lens Diameter (mm)")
LmAC<-lm(F1data$LensD[F1data$Sp=="C.rupestris"]~F1data$TL[F1data$Sp=="C.rupestris"])
abline(LmAC, col="red", lty=2)

plot(F1data$TL[F1data$Sp=="L.nasus"], F1data$LensD[F1data$Sp=="L.nasus"], pch=19, xlab="Total Length (mm)", ylab="Lens Diameter (mm)")
LmAC<-lm(F1data$LensD[F1data$Sp=="L.nasus"]~F1data$TL[F1data$Sp=="L.nasus"])
abline(LmAC, col="red", lty=2)

plot(F1data$TL[F1data$Sp=="S.acanthias"], F1data$LensD[F1data$Sp=="S.acanthias"], pch=19, xlab="Total Length (mm)", ylab="Lens Diameter (mm)")
LmAC<-lm(F1data$LensD[F1data$Sp=="S.acanthias"]~F1data$TL[F1data$Sp=="S.acanthias"])
abline(LmAC, col="red", lty=2)


#################################################Fig 3: A.carbo lens transects

F3data<- read.table("Acarbo_lens.txt", header = TRUE, fill=TRUE)

######creating sequences for second x axis
plotr<-c(-4,-2,0,2,4)
radius<-c(4,2,0,2,4)
TL<-round(((2*radius)--3.713)/0.0185,0)



par(mfrow=c(2,4))
par(mar=c(9,5,5,5))

plot(F3data$Radius1[F3data$FishID=="M113"], F3data$d13C[F3data$FishID=="M113"], pch=19, col="blue", type="o", ylim=c(-21, -17), xlab="Lens radius (mm)", ylab=expression(paste(delta^{13},"C")))
par(new=TRUE)
plot(F3data$Radius1[F3data$FishID=="M113"], F3data$d15N[F3data$FishID=="M113"], pch=21, col="red", type="o", ylim=c(8,18), axes=FALSE, xlab=NA, ylab=NA)
axis(side=4)
mtext(side=4, line = 3, expression(paste(delta^{15},"N")), cex=0.75)
axis(1, line=5, at=plotr, labels=TL)
mtext(side=1, line = 8, "Total length (mm)", cex=0.75)


plot(F3data$Radius1[F3data$FishID=="C400"], F3data$d13C[F3data$FishID=="C400"], pch=19, col="blue", type="o", ylim=c(-21, -17), xlab="Lens radius (mm)", ylab=expression(paste(delta^{13},"C")))
par(new=TRUE)
plot(F3data$Radius1[F3data$FishID=="C400"], F3data$d15N[F3data$FishID=="C400"], pch=21, col="red", type="o", ylim=c(8,18), axes=FALSE, xlab=NA, ylab=NA)
axis(side=4)
mtext(side=4, line = 3, expression(paste(delta^{15},"N")), cex=0.75)
axis(1, line=5, at=plotr, labels=TL)
mtext(side=1, line = 8, "Total length (mm)", cex=0.75)


plot(F3data$Radius1[F3data$FishID=="C402"], F3data$d13C[F3data$FishID=="C402"], pch=19, col="blue", type="o", ylim=c(-21, -17), xlab="Lens radius (mm)", ylab=expression(paste(delta^{13},"C")))
par(new=TRUE)
plot(F3data$Radius1[F3data$FishID=="C402"], F3data$d15N[F3data$FishID=="C402"], pch=21, col="red", type="o", ylim=c(8,18), axes=FALSE, xlab=NA, ylab=NA)
axis(side=4)
mtext(side=4, line = 3,expression(paste(delta^{15},"N")), cex=0.75)
axis(1, line=5, at=plotr, labels=TL)
mtext(side=1, line = 8, "Total length (mm)", cex=0.75)



plot(F3data$Radius1[F3data$FishID=="C404"], F3data$d13C[F3data$FishID=="C404"], pch=19, col="blue", type="o", ylim=c(-21, -17), xlab="Lens radius (mm)", ylab=expression(paste(delta^{13},"C")))
par(new=TRUE)
plot(F3data$Radius1[F3data$FishID=="C404"], F3data$d15N[F3data$FishID=="C404"], pch=21, col="red", type="o", ylim=c(8,18), axes=FALSE, xlab=NA, ylab=NA)
axis(side=4)
mtext(side=4, line = 3, expression(paste(delta^{15},"N")), cex=0.75)
axis(1, line=5, at=plotr, labels=TL)
mtext(side=1, line = 8, "Total length (mm)", cex=0.75)


plot(F3data$Radius1[F3data$FishID=="C405"], F3data$d13C[F3data$FishID=="C405"], pch=19, col="blue", type="o", ylim=c(-21, -17), xlab="Lens radius (mm)", ylab=expression(paste(delta^{13},"C")))
par(new=TRUE)
plot(F3data$Radius1[F3data$FishID=="C405"], F3data$d15N[F3data$FishID=="C405"], pch=21, col="red", type="o", ylim=c(8,18), axes=FALSE, xlab=NA, ylab=NA)
axis(side=4)
mtext(side=4, line = 3, expression(paste(delta^{15},"N")), cex=0.75)
axis(1, line=5, at=plotr, labels=TL)
mtext(side=1, line = 8, "Total length (mm)", cex=0.75)

plot(F3data$Radius1[F3data$FishID=="C406"], F3data$d13C[F3data$FishID=="C406"], pch=19, col="blue", type="o", ylim=c(-21, -17), xlab="Lens radius (mm)", ylab=expression(paste(delta^{13},"C")))
par(new=TRUE)
plot(F3data$Radius1[F3data$FishID=="C406"], F3data$d15N[F3data$FishID=="C406"], pch=21, col="red", type="o", ylim=c(8,18), axes=FALSE, xlab=NA, ylab=NA)
axis(side=4)
mtext(side=4, line = 3, expression(paste(delta^{15},"N")), cex=0.75)
axis(1, line=5, at=plotr, labels=TL)
mtext(side=1, line = 8, "Total length (mm)", cex=0.75)


plot(F3data$Radius1[F3data$FishID=="C512"], F3data$d13C[F3data$FishID=="C512"], pch=19, col="blue", type="o", ylim=c(-21, -17), xlab="Lens radius (mm)", ylab=expression(paste(delta^{13},"C")))
par(new=TRUE)
plot(F3data$Radius1[F3data$FishID=="C512"], F3data$d15N[F3data$FishID=="C512"], pch=21, col="red", type="o", ylim=c(8,18), axes=FALSE, xlab=NA, ylab=NA)
axis(side=4)
mtext(side=4, line = 3, expression(paste(delta^{15},"N")), cex=0.75)
axis(1, line=5, at=plotr, labels=TL)
mtext(side=1, line = 8, "Total length (mm)", cex=0.75)


plot(F3data$Radius1[F3data$FishID=="C515"], F3data$d13C[F3data$FishID=="C515"], pch=19, col="blue", type="o", ylim=c(-21, -17), xlab="Lens radius (mm)", ylab=expression(paste(delta^{13},"C")))
par(new=TRUE)
plot(F3data$Radius1[F3data$FishID=="C515"], F3data$d15N[F3data$FishID=="C515"], pch=21, col="red", type="o", ylim=c(8,18), axes=FALSE, xlab=NA, ylab=NA)
axis(side=4)
mtext(side=4, line = 3, expression(paste(delta^{15},"N")), cex=0.75)
axis(1, line=5, at=plotr, labels=TL)
mtext(side=1, line = 8, "Total length (mm)", cex=0.75)

#############################################Fig 4

F4data<- read.table("lensCore.txt", header = TRUE, fill=TRUE)


par(mar=c(5,5,5,5))
par(mfrow=c(1,1))

plot(F4data$d13C, F4data$d15N, pch=19, cex=1.5, col=as.factor(F4data$Species), xlab=expression(paste(delta^{13},"C")), ylab=expression(paste(delta^{15},"N")))
XCrup13C<-mean(F4data$d13C[F4data$Species=="grenadier"])
SCrup13C<-sd(F4data$d13C[F4data$Species=="grenadier"])

XCrup15N<-mean(F4data$d15N[F4data$Species=="grenadier"])
SCrup15N<-sd(F4data$d15N[F4data$Species=="grenadier"])


XAcarb13C<-mean(F4data$d13C[F4data$Species=="scabbard"])
SAcarb13C<-sd(F4data$d13C[F4data$Species=="scabbard"])

XAcarb15N<-mean(F4data$d15N[F4data$Species=="scabbard"])
SAcarb15N<-sd(F4data$d15N[F4data$Species=="scabbard"])


XLnasus13C<-mean(F4data$d13C[F4data$Species=="porbeagle"])
SLnasus13C<-sd(F4data$d13C[F4data$Species=="porbeagle"])

XLnasus15N<-mean(F4data$d15N[F4data$Species=="porbeagle"])
SLnasus15N<-sd(F4data$d15N[F4data$Species=="porbeagle"])

points(XCrup13C, XCrup15N, col=1, pch=25, cex=3)
arrows(XCrup13C, XCrup15N, XCrup13C-SCrup13C, XCrup15N,code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=1)
arrows(XCrup13C, XCrup15N, XCrup13C+SCrup13C, XCrup15N,code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=1)
arrows(XCrup13C, XCrup15N, XCrup13C,XCrup15N-SCrup15N, code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=1)
arrows(XCrup13C, XCrup15N, XCrup13C,XCrup15N+SCrup15N, code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=1)


points(XLnasus13C, XLnasus15N, col=2, pch=25, cex=3)

arrows(XLnasus13C, XLnasus15N, XLnasus13C-SLnasus13C, XLnasus15N,code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=2)
arrows(XLnasus13C, XLnasus15N, XLnasus13C+SLnasus13C, XLnasus15N,code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=2)
arrows(XLnasus13C, XLnasus15N, XLnasus13C,XLnasus15N-SLnasus15N, code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=2)
arrows(XLnasus13C, XLnasus15N, XLnasus13C,XLnasus15N+SLnasus15N, code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=2)


points(XAcarb13C, XAcarb15N, col=3, pch=25, cex=3)

arrows(XAcarb13C, XAcarb15N, XAcarb13C-SAcarb13C, XAcarb15N,code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=3)
arrows(XAcarb13C, XAcarb15N, XAcarb13C+SAcarb13C, XAcarb15N,code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=3)
arrows(XAcarb13C, XAcarb15N, XAcarb13C,XAcarb15N-SAcarb15N, code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=3)
arrows(XAcarb13C, XAcarb15N, XAcarb13C,XAcarb15N+SAcarb15N, code=3,lwd=0.5, angle=90, length=0.05, lty=1, col=3)


#############################################Fig 5

F5data<- read.table("Embryo.txt", header = TRUE, fill=TRUE)

par(mfrow=c(1,2))

boxplot(F5data$d13Cc~F5data$Tissue,  ylab=expression(paste(delta^{13},"C")), col=c("white", "light grey"), outpch=NA,)
stripchart(F5data$d13Cc~F5data$Tissue, vertical=TRUE, method="jitter", pch=21, col="black", bg="black", add=TRUE)

boxplot(F5data$d15N~F5data$Tissue,  ylab=expression(paste(delta^{15},"N")), col=c("white", "light grey"), outpch=NA,)
stripchart(F5data$d15N~F5data$Tissue, vertical=TRUE, method="jitter", pch=21, col="black", bg="black",  add=TRUE)

dev.off()
d13CXm<-mean(F5data$d13Cc[F5data$Tissue=="M"])
d13CSm<-sd(F5data$d13Cc[F5data$Tissue=="M"])

d15NXm<-mean(F5data$d15N[F5data$Tissue=="M"])
d15NSm<-sd(F5data$d15N[F5data$Tissue=="M"])

d13CXl<-mean(F5data$d13Cc[F5data$Tissue=="L"])
d13CSl<-sd(F5data$d13Cc[F5data$Tissue=="L"])


d15NXl<-mean(F5data$d15N[F5data$Tissue=="L"])
d15NSl<-sd(F5data$d15N[F5data$Tissue=="L"])

t13C<-t.test(F5data$d13Cc[F5data$Tissue=="M"], F5data$d13Cc[F5data$Tissue=="L"], paired=TRUE)
t15N<-t.test(F5data$d15N[F5data$Tissue=="M"], F5data$d15N[F5data$Tissue=="L"], paired=TRUE)

#############################################Fig 6

F6data<- read.table("CrupL_M.txt", header = TRUE, fill=TRUE)

par(mfrow=c(1,2))

boxplot(F6data$d13C~F6data$tissue,  ylab=expression(paste(delta^{13},"C")), col=c("white", "light grey"), outpch=NA,)
stripchart(F6data$d13C~F6data$tissue, vertical=TRUE, method="jitter", pch=21, col="black", bg="black", add=TRUE)

boxplot(F6data$d15N~F6data$tissue,  ylab=expression(paste(delta^{15},"N")), col=c("white", "light grey"), outpch=NA,)
stripchart(F6data$d15N~F6data$tissue, vertical=TRUE, method="jitter", pch=21, col="black", bg="black",  add=TRUE)